rs2844627

Variant names:

• chr6-31261685-C-T
• rs2844627

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.198 in 151,664 control chromosomes in the GnomAD database, including 3,546 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3546 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30071 AN: 151546 Hom.: 3546 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.196

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.198 AC: 30074 AN: 151664 Hom.: 3546 Cov.: 31 AF XY: 0.194 AC XY: 14358 AN XY: 74074

African (AFR) AF: 0.131 AC: 5420 AN: 41448

American (AMR) AF: 0.146 AC: 2234 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3470

East Asian (EAS) AF: 0.0554 AC: 281 AN: 5072

South Asian (SAS) AF: 0.189 AC: 894 AN: 4728

European-Finnish (FIN) AF: 0.175 AC: 1842 AN: 10512

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17325 AN: 67872

Other (OTH) AF: 0.194 AC: 408 AN: 2104

Alfa AF: 0.209 Hom.: 1152

Bravo AF: 0.193

Asia WGS AF: 0.124 AC: 432 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.8
DANN	Benign	0.75
PhyloP100		0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2844627; hg19: chr6-31229462;